Fst matrix 2017 samples

##         TB17  PWS17   SS17   BC17   WA17   CA17
## TB17  0.0000 0.2799 0.2744 0.3334 0.2777 0.3504
## PWS17 0.2799 0.0000 0.0096 0.0164 0.0197 0.0488
## SS17  0.2744 0.0096 0.0000 0.0116 0.0132 0.0567
## BC17  0.3334 0.0164 0.0116 0.0000 0.0213 0.0461
## WA17  0.2777 0.0197 0.0132 0.0213 0.0000 0.0681
## CA17  0.3504 0.0488 0.0567 0.0461 0.0681 0.0000

Note: Very low divergence between CA and BC. Also, much higher divergence between CA and WA than CA and PWS.

Fst matrix temporal samples (within population comparisons)

##        PWS91  PWS96  PWS07  PWS17
## PWS91 0.0000 0.0079 0.0126 0.0089
## PWS96 0.0079 0.0000 0.0100 0.0088
## PWS07 0.0126 0.0100 0.0000 0.0131
## PWS17 0.0089 0.0088 0.0131 0.0000

##        TB91   TB96   TB06   TB17
## TB91 0.0000 0.0083 0.0106 0.0092
## TB96 0.0083 0.0000 0.0137 0.0069
## TB06 0.0106 0.0137 0.0000 0.0103
## TB17 0.0092 0.0069 0.0103 0.0000

##        SS96   SS06   SS17
## SS96 0.0000 0.0111 0.0069
## SS06 0.0111 0.0000 0.0111
## SS17 0.0069 0.0111 0.0000

Note: High Fst between PWS91 and PWS07. Also, high Fst between TB91 and TB96 despite low Fst between TB91 and TB06.

Fst and PBS by chromosome (3 population comparison)

BC, WA, and CA (2017)

Note: Very low divergence between BC and CA (as seen in matrix), but very sharp peaks of divergence on chrs 7, 12, 20, 25.

Fst and PBS by chromosome (3 population comparison)

PWS, SS, and CA (2017)

Note: Same peaks of divergence between CA and PWS/SS on chrs 7, 12, 20.

Fst and PBS by chromosome (3 population comparison)

PWS temporal comparisons

Note: Consistent peaks on chr 6 (also true when including PWS17).

Fst and PBS by chromosome (3 population comparison)

TB temporal comparisons

Fst and PBS by chromosome (3 population comparison)

TB, PWS, SS temporal comparisons (1996)

Fst outliers and GO enrichment for Chr 6

## [1] "54 genes (Danio orthologs) within 50kb Fst outlier window (genome-wide mean > 99%ile)"
##  [1] "nrg2b"            "si:dkey-160o24.3" "eif1ad"           "ctsf"            
##  [5] "si:ch73-22a13.3"  "slit3"            "uraha"            "pdcd5"           
##  [9] "mvda"             "cyba"             "tcf25"            "def8"            
## [13] "uacab"            "pias1a"           "copb1"            "rras2"           
## [17] "pacsin3"          "csnk1g1"          "acp2"

GO enrichment for 54 genes

Fst outliers and GO enrichment for CA v PWS chr 7

## [1] "66 genes (Danio orthologs) within 50kb Fst outlier window (genome-wide mean > 99%ile)"
##  [1] "si:ch73-138n13.1"  "kazald3"           "crybb2"           
##  [4] "dok2"              "gfra2a"            "lzts1"            
##  [7] "cox6a1"            "hps4"              "hnf1a"            
## [10] "zgc:162025"        "lrrc75ba"          "ggt5a"            
## [13] "asphd2"            "cabp1a"            "mlec"             
## [16] "pop5"              "olfml2a"           "arpc5la"          
## [19] "golga1"            "si:ch211-158d24.2" "ddx31"            
## [22] "ak8"               "spaca9"            "grin1b"           
## [25] "ptgesl"            "odf2b"             "gle1"             
## [28] "zgc:136963"        "ctu1"              "pxnb"             
## [31] "citb"              "cux2b"             "pptc7b"           
## [34] "med27"             "NTNG2"             "slc23a2"          
## [37] "ccdc92"            "ciao1"             "snrnp200"         
## [40] "slc20a1a"          "vgll4l"            "syn1"             
## [43] "gapvd1"            "lmx1bb"            "zbtb34"           
## [46] "ralgps1"           "angptl2b"          "RNF122"           
## [49] "inpp5l"            "nkx6.3"            "tmem127"          
## [52] "es1"               "igsf9b"            "bnip3la"          
## [55] "LRRTM4"            "lrrtm4l2"          "vsig8b"           
## [58] "dock5"             "specc1la"          "adora2aa"         
## [61] "upb1"              "gucd1"             "snrpd3"           
## [64] "p2rx4b"            "p2rx7"

GO enrichment for 66 genes